PeptideAtlas is a multi-organism, publicly accessible compendium
of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
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Mass spectrometer output files are collected for human, mouse,
yeast, and several other organisms, and searched using the latest search
engines and protein sequences. All results of sequence and spectral library
searching are subsequently processed through the
Trans Proteomic Pipeline to
derive a probability of correct identification for all results in a uniform
manner to insure a high quality database, along with false discovery rates
at the whole atlas level. Results may be queried and browsed at the
PeptideAtlas web site. The raw data, search results, and full builds can
also be downloaded for other uses.

2013-08-15
We researched all human datasets using new search database, which includes CompleteProteome and varsplic proteins.
A list of new human builds based on new search results have been made available, such as Human 2013-08 and Human Others 2013-08.

2013-06-13
First two C. albicans builds,
C. albicans 2011-12
and
C. albicans 2012-01 PTM
are now publicly available. A paper about both builds has been submitted to the special issue on microbial proteomics of the Journal of Proteomics.

2012-04-27:
First Cow PeptideAtlas is now available to
search.
All data including any formats can be download from our repository site.

2012-03-28:
New Human PeptideAtlas is now available to
search.
5 cell line data sets from recent publications, Nagaraj et al. 2011, Beck et al. 2011, Munoz et al. 2011,
Sharma et al. 2011, and Geiger et al. 2012 have been added to this build. For the older data sets, only the
experiments searched with decoy database are included in order to get a good estimate of decoy FDR. Those not searched with decoy database will be researched, and add to build later.

2011-09-27:
The PeptideAtlas SRM Experiment Library (
PASSEL) is now available for general use. Thus far
it contains only a few public experiments, but several datasets are
under review and will become public upon acceptance. We encourage
submissions
of SRM experiment datasets.

2011-09-13:
Human Brain PeptideAtlas is now available to
search. Raw data is avaiable to
download from PeptideAtlas
repository. The build is available to download.

2011-05-14:
First HoneyBee PeptideAtlas is now available to
search.
The paper is submitted to the BioMed Central and under review. Raw data is avaiable to download from PeptideAtlas repository. The PeptideAtlas build for Honeybee is available to download.

2010-07: The latest versions of Human, Mouse, Drosophila, and Celegans builds are now
available at the
PeptideAtlas.
Version 57 of the EnsEMBL is used for the peptides mapping in all of the new builds.

2010-03:
Members of the PeptideAtlas team have recently published
mspecLINE, a
web application
that allows researchers to explore relationships between human diseases and the observed proteome.

2010-02:
For the first time, a Mouse PeptideAtlas build,
based on 64 samples from a variety of tissues and subcellular
compartments, is available to
search.

Related Resources

PeptideAtlas is a product of the Seattle Proteome Center (SPC), a
highly interactive, multi-disciplinary group aiming to enhance
and develop innovative proteomic technologies and software tools
and apply them to
biological questions relevant to heart, lung, blood, and sleep.

This project has been funded in part with Federal funds from
the National Heart, Lung, and Blood Institute, National
Institutes of Health, under contract No. N01-HV-28179.

PeptideAtlas is a module within SBEAMS, the Systems Biology Experiment Management
System.